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Chi L, Liu C, Gribonika I, Gschwend J, Corral D, Han SJ, Lim AI, Rivera CA, Link VM, Wells AC, Bouladoux N, Collins N, Lima-Junior DS, Enamorado M, Rehermann B, Laffont S, Guéry JC, Tussiwand R, Schneider C, Belkaid Y. Sexual dimorphism in skin immunity is mediated by an androgen-ILC2-dendritic cell axis. Science 2024; 384:eadk6200. [PMID: 38574174 DOI: 10.1126/science.adk6200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
Males and females exhibit profound differences in immune responses and disease susceptibility. However, the factors responsible for sex differences in tissue immunity remain poorly understood. Here, we uncovered a dominant role for type 2 innate lymphoid cells (ILC2s) in shaping sexual immune dimorphism within the skin. Mechanistically, negative regulation of ILC2s by androgens leads to a reduction in dendritic cell accumulation and activation in males, along with reduced tissue immunity. Collectively, our results reveal a role for the androgen-ILC2-dendritic cell axis in controlling sexual immune dimorphism. Moreover, this work proposes that tissue immune set points are defined by the dual action of sex hormones and the microbiota, with sex hormones controlling the strength of local immunity and microbiota calibrating its tone.
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Affiliation(s)
- Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Inta Gribonika
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia Gschwend
- Institute of Physiology, University of Zurich, CH-8057 Zürich, Switzerland
| | - Dan Corral
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claudia A Rivera
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandria C Wells
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Djalma S Lima-Junior
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie Laffont
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, Toulouse, France
| | - Jean-Charles Guéry
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, Toulouse, France
| | - Roxane Tussiwand
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Kulalert W, Wells AC, Link VM, Lim AI, Bouladoux N, Nagai M, Harrison OJ, Kamenyeva O, Kabat J, Enamorado M, Chiu IM, Belkaid Y. The neuroimmune CGRP-RAMP1 axis tunes cutaneous adaptive immunity to the microbiota. Proc Natl Acad Sci U S A 2024; 121:e2322574121. [PMID: 38451947 PMCID: PMC10945812 DOI: 10.1073/pnas.2322574121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 03/09/2024] Open
Abstract
The somatosensory nervous system surveils external stimuli at barrier tissues, regulating innate immune cells under infection and inflammation. The roles of sensory neurons in controlling the adaptive immune system, and more specifically immunity to the microbiota, however, remain elusive. Here, we identified a mechanism for direct neuroimmune communication between commensal-specific T lymphocytes and somatosensory neurons mediated by the neuropeptide calcitonin gene-related peptide (CGRP) in the skin. Intravital imaging revealed that commensal-specific T cells are in close proximity to cutaneous nerve fibers in vivo. Correspondingly, we observed upregulation of the receptor for the neuropeptide CGRP, RAMP1, in CD8+ T lymphocytes induced by skin commensal colonization. The neuroimmune CGRP-RAMP1 signaling axis functions in commensal-specific T cells to constrain Type 17 responses and moderate the activation status of microbiota-reactive lymphocytes at homeostasis. As such, modulation of neuroimmune CGRP-RAMP1 signaling in commensal-specific T cells shapes the overall activation status of the skin epithelium, thereby impacting the outcome of responses to insults such as wounding. The ability of somatosensory neurons to control adaptive immunity to the microbiota via the CGRP-RAMP1 axis underscores the various layers of regulation and multisystem coordination required for optimal microbiota-reactive T cell functions under steady state and pathology.
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Affiliation(s)
- Warakorn Kulalert
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Alexandria C. Wells
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Verena M. Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
- National Institute of Allergy and Infectious Diseases Microbiome Program, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Motoyoshi Nagai
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Oliver J. Harrison
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Olena Kamenyeva
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Juraj Kabat
- Biological Imaging Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
- Kimberly and Eric J. Waldman Department of Dermatology, Mark Lebwohl Center for Neuroinflammation and Sensation, Marc and Jennifer Lipschultz Precision Immunology Institute, and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Isaac M. Chiu
- Department of Immunology, Harvard Medical School, Boston, MA02115
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
- National Institute of Allergy and Infectious Diseases Microbiome Program, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
- Unite Metaorganisme, Immunology Department, Pasteur Institute, 75015 Paris, France
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Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD, Belkaid Y. Author Correction: Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Nat Med 2024:10.1038/s41591-024-02884-0. [PMID: 38409594 DOI: 10.1038/s41591-024-02884-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Affiliation(s)
- Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kyu Lee Han
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
- Center for Cellular Engineering, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Amber B Courville
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Burns
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kevin D Hall
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
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Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD, Belkaid Y. Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Nat Med 2024; 30:560-572. [PMID: 38291301 PMCID: PMC10878979 DOI: 10.1038/s41591-023-02761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
Nutrition has broad impacts on all physiological processes. However, how nutrition affects human immunity remains largely unknown. Here we explored the impact of a dietary intervention on both immunity and the microbiota by performing a post hoc analysis of a clinical trial in which each of the 20 participants sequentially consumed vegan or ketogenic diets for 2 weeks ( NCT03878108 ). Using a multiomics approach including multidimensional flow cytometry, transcriptomic, proteomic, metabolomic and metagenomic datasets, we assessed the impact of each diet, and dietary switch, on host immunity and the microbiota. Our data revealed that overall, a ketogenic diet was associated with a significant upregulation of pathways and enrichment in cells associated with the adaptive immune system. In contrast, a vegan diet had a significant impact on the innate immune system, including upregulation of pathways associated with antiviral immunity. Both diets significantly and differentially impacted the microbiome and host-associated amino acid metabolism, with a strong downregulation of most microbial pathways following ketogenic diet compared with baseline and vegan diet. Despite the diversity of participants, we also observed a tightly connected network between datasets driven by compounds associated with amino acids, lipids and the immune system. Collectively, this work demonstrates that in diverse participants 2 weeks of controlled dietary intervention is sufficient to significantly and divergently impact host immunity, which could have implications for precision nutritional interventions. ClinicalTrials.gov registration: NCT03878108 .
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Affiliation(s)
- Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kyu Lee Han
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
- Center for Cellular Engineering, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Amber B Courville
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Burns
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kevin D Hall
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
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Abe Y, Kofman ER, Ouyang Z, Cruz-Becerra G, Spann NJ, Seidman JS, Troutman TD, Stender JD, Taylor H, Fan W, Link VM, Shen Z, Sakai J, Downes M, Evans RM, Kadonaga JT, Rosenfeld MG, Glass CK. A TLR4/TRAF6-dependent signaling pathway mediates NCoR coactivator complex formation for inflammatory gene activation. Proc Natl Acad Sci U S A 2024; 121:e2316104121. [PMID: 38165941 PMCID: PMC10786282 DOI: 10.1073/pnas.2316104121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
The nuclear receptor corepressor (NCoR) forms a complex with histone deacetylase 3 (HDAC3) that mediates repressive functions of unliganded nuclear receptors and other transcriptional repressors by deacetylation of histone substrates. Recent studies provide evidence that NCoR/HDAC3 complexes can also exert coactivator functions in brown adipocytes by deacetylating and activating PPARγ coactivator 1α (PGC1α) and that signaling via receptor activator of nuclear factor kappa-B (RANK) promotes the formation of a stable NCoR/HDAC3/PGC1β complex that coactivates nuclear factor kappa-B (NFκB)- and activator protein 1 (AP-1)-dependent genes required for osteoclast differentiation. Here, we demonstrate that activation of Toll-like receptor (TLR) 4, but not TLR3, the interleukin 4 (IL4) receptor nor the Type I interferon receptor, also promotes assembly of an NCoR/HDAC3/PGC1β coactivator complex. Receptor-specific utilization of TNF receptor-associated factor 6 (TRAF6) and downstream activation of extracellular signal-regulated kinase 1 (ERK1) and TANK-binding kinase 1 (TBK1) accounts for the common ability of RANK and TLR4 to drive assembly of an NCoR/HDAC3/PGC1β complex in macrophages. ERK1, the p65 component of NFκB, and the p300 histone acetyltransferase (HAT) are also components of the induced complex and are associated with local histone acetylation and transcriptional activation of TLR4-dependent enhancers and promoters. These observations identify a TLR4/TRAF6-dependent signaling pathway that converts NCoR from a corepressor of nuclear receptors to a coactivator of NFκB and AP-1 that may be relevant to functions of NCoR in other developmental and homeostatic processes.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Eric R. Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Stem Cell Program, University of California San Diego, La Jolla, CA92093
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA92093
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Nathanael J. Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Jason S. Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Ty D. Troutman
- Department of Medicine, University of California San Diego, La Jolla, CA92093
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH45229
| | - Joshua D. Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Havilah Taylor
- Department and School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Verena M. Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Munich82152, Germany
| | - Zeyang Shen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA92093
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo153-8904, Japan
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - Ronald M. Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA92037
| | - James T. Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA92093
| | - Michael G. Rosenfeld
- Department and School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
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Kulalert W, Wells AC, Link VM, Lim AI, Bouladoux N, Nagai M, Harrison OJ, Kamenyeva O, Kabat J, Enamorado M, Chiu IM, Belkaid Y. The neuroimmune CGRP-RAMP1 axis tunes cutaneous adaptive immunity to the microbiota. bioRxiv 2023:2023.12.26.573358. [PMID: 38234748 PMCID: PMC10793430 DOI: 10.1101/2023.12.26.573358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The somatosensory nervous system surveils external stimuli at barrier tissues, regulating innate immune cells under infection and inflammation. The roles of sensory neurons in controlling the adaptive immune system, and more specifically immunity to the microbiota, however, remain elusive. Here, we identified a novel mechanism for direct neuroimmune communication between commensal-specific T lymphocytes and somatosensory neurons mediated by the neuropeptide Calcitonin Gene-Related Peptide (CGRP) in the skin. Intravital imaging revealed that commensal-specific T cells are in close proximity to cutaneous nerve fibers in vivo . Correspondingly, we observed upregulation of the receptor for the neuropeptide CGRP, RAMP1, in CD8 + T lymphocytes induced by skin commensal colonization. Neuroimmune CGRP-RAMP1 signaling axis functions in commensal-specific T cells to constrain Type 17 responses and moderate the activation status of microbiota-reactive lymphocytes at homeostasis. As such, modulation of neuroimmune CGRP-RAMP1 signaling in commensal-specific T cells shapes the overall activation status of the skin epithelium, thereby impacting the outcome of responses to insults such as wounding. The ability of somatosensory neurons to control adaptive immunity to the microbiota via the CGRP-RAMP1 axis underscores the various layers of regulation and multisystem coordination required for optimal microbiota-reactive T cell functions under steady state and pathology. Significance statement Multisystem coordination at barrier surfaces is critical for optimal tissue functions and integrity, in response to microbial and environmental cues. In this study, we identified a novel neuroimmune crosstalk mechanism between the sensory nervous system and the adaptive immune response to the microbiota, mediated by the neuropeptide CGRP and its receptor RAMP1 on skin microbiota-induced T lymphocytes. The neuroimmune CGPR-RAMP1 axis constrains adaptive immunity to the microbiota and overall limits the activation status of the skin epithelium, impacting tissue responses to wounding. Our study opens the door to a new avenue to modulate adaptive immunity to the microbiota utilizing neuromodulators, allowing for a more integrative and tailored approach to harnessing microbiota-induced T cells to promote barrier tissue protection and repair.
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Han SJ, Stacy A, Corral D, Link VM, De Siqueira MK, Chi L, Teijeiro A, Yong DS, Perez-Chaparro PJ, Bouladoux N, Lim AI, Enamorado M, Belkaid Y, Collins N. Microbiota configuration determines nutritional immune optimization. Proc Natl Acad Sci U S A 2023; 120:e2304905120. [PMID: 38011570 DOI: 10.1073/pnas.2304905120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/29/2023] Open
Abstract
Mild or transient dietary restriction (DR) improves many aspects of health and aging. Emerging evidence from us and others has demonstrated that DR also optimizes the development and quality of immune responses. However, the factors and mechanisms involved remain to be elucidated. Here, we propose that DR-induced optimization of immunological memory requires a complex cascade of events involving memory T cells, the intestinal microbiota, and myeloid cells. Our findings suggest that DR enhances the ability of memory T cells to recruit and activate myeloid cells in the context of a secondary infection. Concomitantly, DR promotes the expansion of commensal Bifidobacteria within the large intestine, which produce the short-chain fatty acid acetate. Acetate conditioning of the myeloid compartment during DR enhances the capacity of these cells to kill pathogens. Enhanced host protection during DR is compromised when Bifidobacteria expansion is prevented, indicating that microbiota configuration and function play an important role in determining immune responsiveness to this dietary intervention. Altogether, our study supports the idea that DR induces both memory T cells and the gut microbiota to produce distinct factors that converge on myeloid cells to promote optimal pathogen control. These findings suggest that nutritional cues can promote adaptation and co-operation between multiple immune cells and the gut microbiota, which synergize to optimize immunity and protect the collective metaorganism.
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Affiliation(s)
- Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Dan Corral
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | | | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Ana Teijeiro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Daniel S Yong
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - P Juliana Perez-Chaparro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
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8
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Bennett H, Troutman TD, Zhou E, Spann NJ, Link VM, Seidman JS, Nickl CK, Abe Y, Sakai M, Pasillas MP, Marlman JM, Guzman C, Hosseini M, Schnabl B, Glass CK. Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes. Nat Immunol 2023; 24:1825-1838. [PMID: 37735593 PMCID: PMC10602851 DOI: 10.1038/s41590-023-01631-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Noncoding genetic variation drives phenotypic diversity, but underlying mechanisms and affected cell types are incompletely understood. Here, investigation of effects of natural genetic variation on the epigenomes and transcriptomes of Kupffer cells derived from inbred mouse strains identified strain-specific environmental factors influencing Kupffer cell phenotypes, including leptin signaling in Kupffer cells from a steatohepatitis-resistant strain. Cell-autonomous and non-cell-autonomous effects of genetic variation were resolved by analysis of F1 hybrid mice and cells engrafted into an immunodeficient host. During homeostasis, non-cell-autonomous trans effects of genetic variation dominated control of Kupffer cells, while strain-specific responses to acute lipopolysaccharide injection were dominated by actions of cis-acting effects modifying response elements for lineage-determining and signal-dependent transcription factors. These findings demonstrate that epigenetic landscapes report on trans effects of genetic variation and serve as a resource for deeper analyses into genetic control of transcription in Kupffer cells and macrophages in vitro.
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Affiliation(s)
- Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Division of Allergy and Immunology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Enchen Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christian K Nickl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin M Marlman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carlos Guzman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mojgan Hosseini
- Department of Pathology, University of California, San Diego, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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9
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Abe Y, Kofman ER, Almeida M, Ouyang Z, Ponte F, Mueller JR, Cruz-Becerra G, Sakai M, Prohaska TA, Spann NJ, Resende-Coelho A, Seidman JS, Stender JD, Taylor H, Fan W, Link VM, Cobo I, Schlachetzki JCM, Hamakubo T, Jepsen K, Sakai J, Downes M, Evans RM, Yeo GW, Kadonaga JT, Manolagas SC, Rosenfeld MG, Glass CK. RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression. Mol Cell 2023; 83:3421-3437.e11. [PMID: 37751740 PMCID: PMC10591845 DOI: 10.1016/j.molcel.2023.08.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the NCoR/HDAC3 co-repressor complex to a co-activator of AP-1 and NF-κB target genes that are required for mouse osteoclast differentiation. Accordingly, the dominant function of NCoR/HDAC3 complexes in response to RANK signaling is to activate, rather than repress, gene expression. Mechanistically, RANK signaling promotes RNA-dependent interaction of the transcriptional co-activator PGC1β with the NCoR/HDAC3 complex, resulting in the activation of PGC1β and inhibition of HDAC3 activity for acetylated histone H3. Non-coding RNAs Dancr and Rnu12, which are associated with altered human bone homeostasis, promote NCoR/HDAC3 complex assembly and are necessary for RANKL-induced osteoclast differentiation in vitro. These findings may be prototypic for signal-dependent functions of NCoR in other biological contexts.
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Affiliation(s)
- Yohei Abe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Almeida
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Filipa Ponte
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Grisel Cruz-Becerra
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Biochemistry and Molecular Biology, Nippon Medical School Hospital, Tokyo 113-8602, Japan
| | - Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Resende-Coelho
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Havilah Taylor
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Takao Hamakubo
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo 113-8602, Japan
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James T Kadonaga
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stavros C Manolagas
- Division of Endocrinology and Metabolism, Center for Osteoporosis and Metabolic Bone Diseases, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Orthopedic Surgery, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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10
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Gao Y, Wang Y, Chauss D, Villarino AV, Link VM, Nagashima H, Spinner CA, Koparde VN, Bouladoux N, Abers MS, Break TJ, Chopp LB, Park JH, Zhu J, Wiest DL, Leonard WJ, Lionakis MS, O'Shea JJ, Afzali B, Belkaid Y, Lazarevic V. Transcription factor EGR2 controls homing and pathogenicity of T H17 cells in the central nervous system. Nat Immunol 2023; 24:1331-1344. [PMID: 37443284 PMCID: PMC10500342 DOI: 10.1038/s41590-023-01553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
CD4+ T helper 17 (TH17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic TH17 cells in the central nervous system (CNS) but not that of protective TH17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4+ T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the TH17 cell transcriptional regulatory network and showed high interconnectivity with core TH17 cell-specific transcription factors. Mechanistically, EGR2 enhanced TH17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host's ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic TH17 cells in the CNS.
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Affiliation(s)
- Yuanyuan Gao
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yan Wang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alejandro V Villarino
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIH Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hiroyuki Nagashima
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Camille A Spinner
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vishal N Koparde
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy J Break
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura B Chopp
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Hyun Park
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David L Wiest
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vanja Lazarevic
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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11
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Enamorado M, Kulalert W, Han SJ, Rao I, Delaleu J, Link VM, Yong D, Smelkinson M, Gil L, Nakajima S, Linehan JL, Bouladoux N, Wlaschin J, Kabat J, Kamenyeva O, Deng L, Gribonika I, Chesler AT, Chiu IM, Le Pichon CE, Belkaid Y. Immunity to the microbiota promotes sensory neuron regeneration. Cell 2023; 186:607-620.e17. [PMID: 36640762 DOI: 10.1016/j.cell.2022.12.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Tissue immunity and responses to injury depend on the coordinated action and communication among physiological systems. Here, we show that, upon injury, adaptive responses to the microbiota directly promote sensory neuron regeneration. At homeostasis, tissue-resident commensal-specific T cells colocalize with sensory nerve fibers within the dermis, express a transcriptional program associated with neuronal interaction and repair, and promote axon growth and local nerve regeneration following injury. Mechanistically, our data reveal that the cytokine interleukin-17A (IL-17A) released by commensal-specific Th17 cells upon injury directly signals to sensory neurons via IL-17 receptor A, the transcription of which is specifically upregulated in injured neurons. Collectively, our work reveals that in the context of tissue damage, preemptive immunity to the microbiota can rapidly bridge biological systems by directly promoting neuronal repair, while also identifying IL-17A as a major determinant of this fundamental process.
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Affiliation(s)
- Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Warakorn Kulalert
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Indira Rao
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jérémie Delaleu
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Yong
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margery Smelkinson
- Biological Imaging, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Louis Gil
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saeko Nakajima
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan L Linehan
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Josette Wlaschin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juraj Kabat
- Biological Imaging, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olena Kamenyeva
- Biological Imaging, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liwen Deng
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Inta Gribonika
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander T Chesler
- National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Isaac M Chiu
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Claire E Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Zhang Y, Bailey JT, Xu E, Singh K, Lavaert M, Link VM, D'Souza S, Hafiz A, Cao J, Cao G, Sant'Angelo DB, Sun W, Belkaid Y, Bhandoola A, McGavern DB, Yang Q. Mucosal-associated invariant T cells restrict reactive oxidative damage and preserve meningeal barrier integrity and cognitive function. Nat Immunol 2022; 23:1714-1725. [PMID: 36411380 PMCID: PMC10202031 DOI: 10.1038/s41590-022-01349-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 10/03/2022] [Indexed: 11/22/2022]
Abstract
Increasing evidence indicates close interaction between immune cells and the brain, revising the traditional view of the immune privilege of the brain. However, the specific mechanisms by which immune cells promote normal neural function are not entirely understood. Mucosal-associated invariant T cells (MAIT cells) are a unique type of innate-like T cell with molecular and functional properties that remain to be better characterized. In the present study, we report that MAIT cells are present in the meninges and express high levels of antioxidant molecules. MAIT cell deficiency in mice results in the accumulation of reactive oxidative species in the meninges, leading to reduced expression of junctional protein and meningeal barrier leakage. The presence of MAIT cells restricts neuroinflammation in the brain and preserves learning and memory. Together, our work reveals a new functional role for MAIT cells in the meninges and suggests that meningeal immune cells can help maintain normal neural function by preserving meningeal barrier homeostasis and integrity.
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Affiliation(s)
- Yuanyue Zhang
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jacob T Bailey
- Department of Immunology & Microbial Disease, Albany Medical College, Albany, NY, USA
| | - En Xu
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kunal Singh
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Marieke Lavaert
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shanti D'Souza
- Department of Immunology & Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Alex Hafiz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine and Science, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Derek B Sant'Angelo
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Wei Sun
- Department of Immunology & Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Qi Yang
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
- Rutgers Institute for Translational Medicine and Science, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
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13
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Hu ZI, Link VM, Lima-Junior DS, Delaleu J, Bouladoux N, Han SJ, Collins N, Belkaid Y. Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota. Proc Natl Acad Sci U S A 2022; 119:e2200348119. [PMID: 35727974 PMCID: PMC9245641 DOI: 10.1073/pnas.2200348119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) are essential components of the cancer therapeutic armamentarium. While ICIs have demonstrated remarkable clinical responses, they can be accompanied by immune-related adverse events (irAEs). These inflammatory side effects are of unclear etiology and impact virtually all organ systems, with the most common being sites colonized by the microbiota such as the skin and gastrointestinal tract. Here, we establish a mouse model of commensal bacteria-driven skin irAEs and demonstrate that immune checkpoint inhibition unleashes commensal-specific inflammatory T cell responses. These aberrant responses were dependent on production of IL-17 by commensal-specific T cells and induced pathology that recapitulated the cutaneous inflammation seen in patients treated with ICIs. Importantly, aberrant T cell responses unleashed by ICIs were sufficient to perpetuate inflammatory memory responses to the microbiota months following the cessation of treatment. Altogether, we have established a mouse model of skin irAEs and reveal that ICIs unleash aberrant immune responses against skin commensals, with long-lasting inflammatory consequences.
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Affiliation(s)
- Zishuo Ian Hu
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
- National Cancer Institute, Medical Oncology Fellowship Program, NIH, Bethesda, MD 20892
| | - Verena M. Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Djalma S. Lima-Junior
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Jérémie Delaleu
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
- Microbiome Program, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
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14
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Toropainen A, Stolze LK, Örd T, Whalen MB, Torrell PM, Link VM, Kaikkonen MU, Romanoski CE. Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations. Genome Res 2022; 32:409-424. [PMID: 35193936 PMCID: PMC8896458 DOI: 10.1101/gr.276064.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/06/2022] [Indexed: 11/25/2022]
Abstract
Functional consequences of genetic variation in the noncoding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional noncoding SNPs with effects in human endothelial cells (ECs), we utilized our previous molecular quantitative trait locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional noncoding SNPs. Together with information from genome-wide association studies (GWASs) for vascular disease traits, we tested the ability of 34,344 variants to perturb enhancer function in ECs using the highly multiplexed STARR-seq assay. Of these, 5711 variants validated, whose enriched attributes included: (1) mutations to TF binding motifs for ETS or AP-1 that are regulators of the EC state; (2) location in accessible and H3K27ac-marked EC chromatin; and (3) molQTL associations whereby alleles associate with differences in chromatin accessibility and TF binding across genetically diverse ECs. Next, using pro-inflammatory IL1B as an activator of cell state, we observed robust evidence (>50%) of context-specific SNP effects, underscoring the prevalence of noncoding gene-by-environment (GxE) effects. Lastly, using these cumulative data, we fine-mapped vascular disease loci and highlighted evidence suggesting mechanisms by which noncoding SNPs at two loci affect risk for pulse pressure/large artery stroke and abdominal aortic aneurysm through respective effects on transcriptional regulation of POU4F1 and LDAH. Together, we highlight the attributes and context dependence of functional noncoding SNPs and provide new mechanisms underlying vascular disease risk.
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Affiliation(s)
- Anu Toropainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Lindsey K Stolze
- The Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Arizona 85721, USA.,The Genetics Interdisciplinary Graduate Program, The University of Arizona, Tucson, Arizona 85721, USA
| | - Tiit Örd
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Michael B Whalen
- The Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Arizona 85721, USA
| | - Paula Martí Torrell
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Minna U Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Casey E Romanoski
- The Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, Arizona 85721, USA.,The Genetics Interdisciplinary Graduate Program, The University of Arizona, Tucson, Arizona 85721, USA
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15
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Lim AI, McFadden T, Link VM, Han SJ, Karlsson RM, Stacy A, Farley TK, Lima-Junior DS, Harrison OJ, Desai JV, Lionakis MS, Shih HY, Cameron HA, Belkaid Y. Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring. Science 2021; 373:373/6558/eabf3002. [PMID: 34446580 DOI: 10.1126/science.abf3002] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
The immune system has evolved in the face of microbial exposure. How maternal infection experienced at distinct developmental stages shapes the offspring immune system remains poorly understood. Here, we show that during pregnancy, maternally restricted infection can have permanent and tissue-specific impacts on offspring immunity. Mechanistically, maternal interleukin-6 produced in response to infection can directly impose epigenetic changes on fetal intestinal epithelial stem cells, leading to long-lasting impacts on intestinal immune homeostasis. As a result, offspring of previously infected dams develop enhanced protective immunity to gut infection and increased inflammation in the context of colitis. Thus, maternal infection can be coopted by the fetus to promote long-term, tissue-specific fitness, a phenomenon that may come at the cost of predisposition to inflammatory disorders.
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Affiliation(s)
- Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Taryn McFadden
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rose-Marie Karlsson
- Section on Neuroplasticity, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, Bethesda, MD 20892, USA
| | - Taylor K Farley
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Djalma S Lima-Junior
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Oliver J Harrison
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jigar V Desai
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heather A Cameron
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Section on Neuroplasticity, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology and Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. .,NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Kaulich M, Link VM, Lapek JD, Lee YJ, Glass CK, Gonzalez DJ, Dowdy SF. A Cdk4/6-dependent phosphorylation gradient regulates the early to late G1 phase transition. Sci Rep 2021; 11:14736. [PMID: 34282211 PMCID: PMC8290049 DOI: 10.1038/s41598-021-94200-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/30/2021] [Indexed: 11/29/2022] Open
Abstract
During early G1 phase, Rb is exclusively mono-phosphorylated by cyclin D:Cdk4/6, generating 14 different isoforms with specific binding patterns to E2Fs and other cellular protein targets. While mono-phosphorylated Rb is dispensable for early G1 phase progression, interfering with cyclin D:Cdk4/6 kinase activity prevents G1 phase progression, questioning the role of cyclin D:Cdk4/6 in Rb inactivation. To dissect the molecular functions of cyclin D:Cdk4/6 during cell cycle entry, we generated a single cell reporter for Cdk2 activation, RB inactivation and cell cycle entry by CRISPR/Cas9 tagging endogenous p27 with mCherry. Through single cell tracing of Cdk4i cells, we identified a time-sensitive early G1 phase specific Cdk4/6-dependent phosphorylation gradient that regulates cell cycle entry timing and resides between serum-sensing and cyclin E:Cdk2 activation. To reveal the substrate identity of the Cdk4/6 phosphorylation gradient, we performed whole proteomic and phospho-proteomic mass spectrometry, and identified 147 proteins and 82 phospho-peptides that significantly changed due to Cdk4 inhibition in early G1 phase. In summary, we identified novel (non-Rb) cyclin D:Cdk4/6 substrates that connects early G1 phase functions with cyclin E:Cdk2 activation and Rb inactivation by hyper-phosphorylation.
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Affiliation(s)
- Manuel Kaulich
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. .,Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany.
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John D Lapek
- Department of Pharmacology, University of California San Diego, La Jolla, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yeon J Lee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California San Diego, La Jolla, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Steven F Dowdy
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
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17
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Lima-Junior DS, Krishnamurthy SR, Bouladoux N, Collins N, Han SJ, Chen EY, Constantinides MG, Link VM, Lim AI, Enamorado M, Cataisson C, Gil L, Rao I, Farley TK, Koroleva G, Attig J, Yuspa SH, Fischbach MA, Kassiotis G, Belkaid Y. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota. Cell 2021; 184:3794-3811.e19. [PMID: 34166614 PMCID: PMC8381240 DOI: 10.1016/j.cell.2021.05.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/10/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
The microbiota plays a fundamental role in regulating host immunity. However, the processes involved in the initiation and regulation of immunity to the microbiota remain largely unknown. Here, we show that the skin microbiota promotes the discrete expression of defined endogenous retroviruses (ERVs). Keratinocyte-intrinsic responses to ERVs depended on cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes protein (STING) signaling and promoted the induction of commensal-specific T cells. Inhibition of ERV reverse transcription significantly impacted these responses, resulting in impaired immunity to the microbiota and its associated tissue repair function. Conversely, a lipid-enriched diet primed the skin for heightened ERV- expression in response to commensal colonization, leading to increased immune responses and tissue inflammation. Together, our results support the idea that the host may have co-opted its endogenous virome as a means to communicate with the exogenous microbiota, resulting in a multi-kingdom dialog that controls both tissue homeostasis and inflammation.
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Affiliation(s)
- Djalma S Lima-Junior
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin Y Chen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael G Constantinides
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIH Center for Human Immunology, Bethesda, MD 20896, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christophe Cataisson
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Louis Gil
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Indira Rao
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Taylor K Farley
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, UK
| | | | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Stuart H Yuspa
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Stacy A, Andrade-Oliveira V, McCulloch JA, Hild B, Oh JH, Perez-Chaparro PJ, Sim CK, Lim AI, Link VM, Enamorado M, Trinchieri G, Segre JA, Rehermann B, Belkaid Y. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell 2021; 184:615-627.e17. [PMID: 33453153 PMCID: PMC8786454 DOI: 10.1016/j.cell.2020.12.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/19/2020] [Accepted: 12/08/2020] [Indexed: 01/13/2023]
Abstract
The microbiota shields the host against infections in a process known as colonization resistance. How infections themselves shape this fundamental process remains largely unknown. Here, we show that gut microbiota from previously infected hosts display enhanced resistance to infection. This long-term functional remodeling is associated with altered bile acid metabolism leading to the expansion of taxa that utilize the sulfonic acid taurine. Notably, supplying exogenous taurine alone is sufficient to induce this alteration in microbiota function and enhance resistance. Mechanistically, taurine potentiates the microbiota's production of sulfide, an inhibitor of cellular respiration, which is key to host invasion by numerous pathogens. As such, pharmaceutical sequestration of sulfide perturbs the microbiota's composition and promotes pathogen invasion. Together, this work reveals a process by which the host, triggered by infection, can deploy taurine as a nutrient to nourish and train the microbiota, promoting its resistance to subsequent infection.
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Affiliation(s)
- Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Vinicius Andrade-Oliveira
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ji Hoon Oh
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Juliana Perez-Chaparro
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Choon K Sim
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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19
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Vogel Ciernia A, Link VM, Careaga M, LaSalle J, Ashwood P. Genetic variants drive altered epigenetic regulation of endotoxin response in BTBR macrophages. Brain Behav Immun 2020; 89:20-31. [PMID: 32454135 PMCID: PMC7572655 DOI: 10.1016/j.bbi.2020.05.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/09/2023] Open
Abstract
The BTBR T+Itpr3tf/J (BTBR) mouse has been used as a complex genetic model of Autism Spectrum Disorders (ASD). While the specific mechanisms underlying BTBR behavioral phenotypes are poorly understood, prior studies have implicated profound differences in innate immune system control of pro-inflammatory cytokines. Innate immune activation and elevated pro-inflammatory cytokines are also detected in blood of children with ASD. In this study, we examined how underlying BTBR genetic variants correspond to strain-specific changes in chromatin accessibility, resulting in a pro-inflammatory response specifically in BTBR bone marrow derived macrophages (BMDM). In response to repeated lipopolysaccharide (LPS) treatments, C57BL/6J (C57) BMDM exhibited intact endotoxin tolerance. In contrast, BTBR BMDM exhibited hyper-responsive expression of genes that were normally tolerized in C57. This failure in formation of endotoxin tolerance in BTBR was mirrored at the level of chromatin accessibility. Using ATAC-seq, we specifically identified promoter and enhancer regions with strain-specific differential chromatin accessibility both at baseline and in response to LPS. Regions with strain-specific differences in chromatin accessibility were significantly enriched for BTBR genetic variants, such that an average of 22% of the differential chromatin regions had at least one variant. Together, these results demonstrate that BTBR genetic variants contribute to altered chromatin responsiveness to endotoxin challenge resulting in hyper-responsive innate immunity in BTBR. These findings provide evidence for an interaction between complex genetic variants and differential epigenetic regulation of innate immune responses.
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Affiliation(s)
- Annie Vogel Ciernia
- Department Biochemistry and Molecular Biology, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada V6T2A1, Corresponding author: Annie Vogel Ciernia, Djavad Mowafaghian Centre for Brain Health, 2215 Wesbrook Mall, University of British Columbia, Vancouver, Canada, 604-827-0752,
| | - Verena M. Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA 20892
| | - Milo Careaga
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA 95616
| | - Janine LaSalle
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA 95616
| | - Paul Ashwood
- Department of Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, CA USA 95616
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20
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Constantinides MG, Link VM, Tamoutounour S, Wong AC, Perez-Chaparro PJ, Han SJ, Chen YE, Li K, Farhat S, Weckel A, Krishnamurthy SR, Vujkovic-Cvijin I, Linehan JL, Bouladoux N, Merrill ED, Roy S, Cua DJ, Adams EJ, Bhandoola A, Scharschmidt TC, Aubé J, Fischbach MA, Belkaid Y. MAIT cells are imprinted by the microbiota in early life and promote tissue repair. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.84.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Early-life microbial colonization has been shown to impart long-lasting effects on host fitness. Because mucosal-associated invariant T (MAIT) cells are predominantly located in tissues colonized by the microbiota and characterized by their recognition of microbial-derived riboflavin intermediates, they are thought to be particularly dependent on the microbiota. However, little is known about their development and how they contribute to tissue physiology. MAIT cells accumulated in barrier tissues between 2 and 3 weeks of age, suggesting that MAIT cells develop during a very specific temporal window and in response to defined microbial exposure. The isolation of early-life intestinal commensals and subsequent colonization of neonatal germ-free mice with defined bacteria induced MAIT cell development. Conversely, colonization later in life failed to promote their development within tissues, indicating that microbial exposure must occur during an early-life window. Following their development, MAIT cells represented a dominant type-17 subset in the skin and cutaneous MAIT cells uniquely expressed a transcriptional program associated with tissue repair. Cutaneous MAIT cells responded locally to skin commensals in a manner that required IL-1 and IL-18, as well as MR1-mediated presentation of riboflavin metabolites. Topical application of a riboflavin derivative selectively increased MAIT cells in the skin and was sufficient to promote cutaneous wound healing. Our work demonstrates that MAIT cells are induced during a specific early-life window in response to riboflavin-synthesizing commensals, which permanently imprints the abundance of this subset in tissues, thereby controlling tissue repair and homeostasis.
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Affiliation(s)
| | - Verena M. Link
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Samira Tamoutounour
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | - Seong-Ji Han
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | - Kelin Li
- 4University of North Carolina at Chapel Hill
| | | | | | | | - Ivan Vujkovic-Cvijin
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Jonathan L. Linehan
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Nicolas Bouladoux
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - E. Dean Merrill
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | | | - Avinash Bhandoola
- 8Center for Cancer Research, National Cancer Institute, National Institutes of Health
| | | | | | | | - Yasmine Belkaid
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
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21
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Seidman JS, Troutman TD, Sakai M, Gola A, Spann NJ, Bennett H, Bruni CM, Ouyang Z, Li RZ, Sun X, Vu BT, Pasillas MP, Ego KM, Gosselin D, Link VM, Chong LW, Evans RM, Thompson BM, McDonald JG, Hosseini M, Witztum JL, Germain RN, Glass CK. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity 2020; 52:1057-1074.e7. [PMID: 32362324 DOI: 10.1016/j.immuni.2020.04.001] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023]
Abstract
Tissue-resident and recruited macrophages contribute to both host defense and pathology. Multiple macrophage phenotypes are represented in diseased tissues, but we lack deep understanding of mechanisms controlling diversification. Here, we investigate origins and epigenetic trajectories of hepatic macrophages during diet-induced non-alcoholic steatohepatitis (NASH). The NASH diet induced significant changes in Kupffer cell enhancers and gene expression, resulting in partial loss of Kupffer cell identity, induction of Trem2 and Cd9 expression, and cell death. Kupffer cell loss was compensated by gain of adjacent monocyte-derived macrophages that exhibited convergent epigenomes, transcriptomes, and functions. NASH-induced changes in Kupffer cell enhancers were driven by AP-1 and EGR that reprogrammed LXR functions required for Kupffer cell identity and survival to instead drive a scar-associated macrophage phenotype. These findings reveal mechanisms by which disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct gene expression programs and corresponding functions.
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Affiliation(s)
- Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Anita Gola
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 201892, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cassi M Bruni
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaoli Sun
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - BaoChau T Vu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kaori M Ego
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David Gosselin
- Department of Molecular Medicine, Université Laval, Quebec City, QC, Canada
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Ling-Wa Chong
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bonne M Thompson
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mojgan Hosseini
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Joseph L Witztum
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 201892, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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22
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Constantinides MG, Link VM, Tamoutounour S, Wong AC, Perez-Chaparro PJ, Han SJ, Chen YE, Li K, Farhat S, Weckel A, Krishnamurthy SR, Vujkovic-Cvijin I, Linehan JL, Bouladoux N, Merrill ED, Roy S, Cua DJ, Adams EJ, Bhandoola A, Scharschmidt TC, Aubé J, Fischbach MA, Belkaid Y. MAIT cells are imprinted by the microbiota in early life and promote tissue repair. Science 2020; 366:366/6464/eaax6624. [PMID: 31649166 DOI: 10.1126/science.aax6624] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022]
Abstract
How early-life colonization and subsequent exposure to the microbiota affect long-term tissue immunity remains poorly understood. Here, we show that the development of mucosal-associated invariant T (MAIT) cells relies on a specific temporal window, after which MAIT cell development is permanently impaired. This imprinting depends on early-life exposure to defined microbes that synthesize riboflavin-derived antigens. In adults, cutaneous MAIT cells are a dominant population of interleukin-17A (IL-17A)-producing lymphocytes, which display a distinct transcriptional signature and can subsequently respond to skin commensals in an IL-1-, IL-18-, and antigen-dependent manner. Consequently, local activation of cutaneous MAIT cells promotes wound healing. Together, our work uncovers a privileged interaction between defined members of the microbiota and MAIT cells, which sequentially controls both tissue-imprinting and subsequent responses to injury.
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Affiliation(s)
- Michael G Constantinides
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea C Wong
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P Juliana Perez-Chaparro
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Y Erin Chen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sepideh Farhat
- Department of Dermatology, University of California, San Francisco, CA 94143, USA
| | - Antonin Weckel
- Department of Dermatology, University of California, San Francisco, CA 94143, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan L Linehan
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - E Dean Merrill
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sobhan Roy
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Daniel J Cua
- Merck & Co., Merck Research Laboratories, Palo Alto, CA 94304, USA
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. .,NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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23
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Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y. Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. EMBO J 2020; 39:e103949. [PMID: 32125007 DOI: 10.15252/embj.2019103949] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
Histone H3 lysine-9 di-methylation (H3K9me2) and lysine-27 tri-methylation (H3K27me3) are linked to repression of gene expression, but the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. Here, we report that lysine demethylases 7A (KDM7A) and 6A (UTX) play crucial roles in tumor necrosis factor (TNF)-α signaling in endothelial cells (ECs), where they are regulated by a novel TNF-α-responsive microRNA, miR-3679-5p. TNF-α rapidly induces co-occupancy of KDM7A and UTX at nuclear factor kappa-B (NF-κB)-associated elements in human ECs. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and are both required for activation of NF-κB-dependent inflammatory genes. Chromosome conformation capture-based methods furthermore uncover increased interactions between TNF-α-induced super enhancers at NF-κB-relevant loci, coinciding with KDM7A and UTX recruitments. Simultaneous pharmacological inhibition of KDM7A and UTX significantly reduces leukocyte adhesion in mice, establishing the biological and potential translational relevance of this mechanism. Collectively, these findings suggest that rapid erasure of repressive histone marks by KDM7A and UTX is essential for NF-κB-dependent regulation of genes that control inflammatory responses of ECs.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo, Japan.,Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yusuke Matsui
- Division of Biomedical and Health Informatics, Graduate school of medicine, Nagoya university, Nagoya, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Nao Nagai
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Shuichi Tsutsumi
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo, Japan
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany.,Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mizuko Osaka
- Department of Nutrition in Cardiovascular Disease, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Life Sciences and Bioethics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masayuki Yoshida
- Department of Life Sciences and Bioethics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryo Watanabe
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akashi Taguchi
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Mai Miura
- Isotope Science Center, The University of Tokyo, Tokyo, Japan.,Laboratory for Systems Biology and Medicine, RCAST, The University of Tokyo, Tokyo, Japan
| | - Xiaoan Ruan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Tsuyoshi Inoue
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsushi Furukawa
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Aburatani
- Division of Genome Sciences, RCAST, The University of Tokyo, Tokyo, Japan
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Yijun Ruan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
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24
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Sajti E, Link VM, Ouyang Z, Spann NJ, Westin E, Romanoski CE, Fonseca GJ, Prince LS, Glass CK. Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nat Immunol 2020; 21:221-231. [PMID: 31959980 PMCID: PMC7667722 DOI: 10.1038/s41590-019-0582-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/12/2019] [Indexed: 02/08/2023]
Abstract
The lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey lung tissues. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing their molecular identities and functional potential remain poorly understood. In the present study, systematic evaluation of transcriptomes and open chromatin of alveolar macrophages (AMs), interstitial macrophages (IMs) and lung monocytes from two mouse strains enabled inference of common and cell-specific transcriptional regulators. We provide evidence that these factors drive selection of regulatory landscapes that specify distinct phenotypes of AMs and IMs and entrain qualitatively different responses to toll-like receptor 4 signaling in vivo. These studies reveal a striking divergence in a fundamental innate immune response pathway in AMs and establish a framework for further understanding macrophage diversity in the lung.
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Affiliation(s)
- Eniko Sajti
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, La Jolla, CA, USA.
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emma Westin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular & Molecular Medicine, Bioscience Research Laboratories, University of Arizona, College of Medicine, Tucson, AZ, USA
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, Division of Quantitative Life Sciences, Meakins-Christie Laboratories, McGill University Health Centre, Montreal, Quebec, Canada
| | - Lawrence S Prince
- Department of Pediatrics, University of California San Diego, Rady Children's Hospital, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
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25
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Sakai M, Troutman TD, Seidman JS, Ouyang Z, Spann NJ, Abe Y, Ego KM, Bruni CM, Deng Z, Schlachetzki JCM, Nott A, Bennett H, Chang J, Vu BT, Pasillas MP, Link VM, Texari L, Heinz S, Thompson BM, McDonald JG, Geissmann F, Glass CK. Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. Immunity 2019; 51:655-670.e8. [PMID: 31587991 DOI: 10.1016/j.immuni.2019.09.002] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/27/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022]
Abstract
Tissue environment plays a powerful role in establishing and maintaining the distinct phenotypes of resident macrophages, but the underlying molecular mechanisms remain poorly understood. Here, we characterized transcriptomic and epigenetic changes in repopulating liver macrophages following acute Kupffer cell depletion as a means to infer signaling pathways and transcription factors that promote Kupffer cell differentiation. We obtained evidence that combinatorial interactions of the Notch ligand DLL4 and transforming growth factor-b (TGF-β) family ligands produced by sinusoidal endothelial cells and endogenous LXR ligands were required for the induction and maintenance of Kupffer cell identity. DLL4 regulation of the Notch transcriptional effector RBPJ activated poised enhancers to rapidly induce LXRα and other Kupffer cell lineage-determining factors. These factors in turn reprogrammed the repopulating liver macrophage enhancer landscape to converge on that of the original resident Kupffer cells. Collectively, these findings provide a framework for understanding how macrophage progenitor cells acquire tissue-specific phenotypes.
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Affiliation(s)
- Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kaori M Ego
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cassi M Bruni
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zihou Deng
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexi Nott
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - BaoChau T Vu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich 82152, Germany
| | - Lorane Texari
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bonne M Thompson
- Department of Molecular Genetics, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, Center for Human Nutrition, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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26
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Sakai M, Troutman TD, Seidman JS, Ouyang Z, Spann NJ, Abe Y, Ego K, Bruni CM, Schlachetzki JCM, Nott A, Bennett H, Chang J, Vu BT, Pasillas M, Link VM, Texari L, Heinz S, Glass CK. Deciphering liver environmental signaling pathways for Kupffer cell identity. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.187.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Functional specialization of tissue resident macrophages occurs through environmental signals controlling activity and/or expression of transcription factors. Kupffer cells are resident macrophages in the hepatic sinusoids and have critical roles in the innate immune response and iron metabolism. Here, we characterize transcriptomic and epigenetic changes in repopulating liver macrophages following acute Kupffer cell depletion as a means to infer signaling pathways and transcription factors that promote Kupffer cell differentiation. Nr1h3 encoding LXRα is rapidly and highly induced in repopulating liver macrophages, suggesting its induction plays a crucial role in Kupffer cell differentiation. Restricted deletion of Nr1h3 in Kupffer cells reveal that it is required for shaping the Kupffer cell-specific enhancer landscape. Further, we obtain evidence that combinatorial interactions of DLL4 and TGF-β/BMP produced by sinusoidal endothelial cells and endogenous LXR ligands are required for the induction and maintenance of Kupffer cell identity. DLL4 regulation of RBPJ through Notch signaling plays a key role in activating poised enhancers to rapidly induce LXRα and other Kupffer cell lineage-determining factors. These factors in turn reprogram the repopulating liver macrophage enhancer landscape to converge on that of the original resident Kupffer cells. Using molecules which mimic these liver environment signals, we show that it is possible to induce Kupffer cell-specific genes in mouse bone marrow progenitor cells and human monocytes in vitro. Collectively, these findings provide a framework for understanding how macrophage progenitor cells acquire tissue-specific phenotypes.
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Affiliation(s)
- Mashito Sakai
- 1Department of Cellular and Molecular Medicine, UCSD
| | | | | | | | | | - Yohei Abe
- 1Department of Cellular and Molecular Medicine, UCSD
| | - Kaori Ego
- 1Department of Cellular and Molecular Medicine, UCSD
| | | | | | - Alexi Nott
- 1Department of Cellular and Molecular Medicine, UCSD
| | | | | | - BaoChau T. Vu
- 1Department of Cellular and Molecular Medicine, UCSD
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27
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Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun 2019; 10:414. [PMID: 30679424 PMCID: PMC6345992 DOI: 10.1038/s41467-018-08236-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
Mechanisms by which members of the AP-1 family of transcription factors play non-redundant biological roles despite recognizing the same DNA sequence remain poorly understood. To address this question, here we investigate the molecular functions and genome-wide DNA binding patterns of AP-1 family members in primary and immortalized mouse macrophages. ChIP-sequencing shows overlapping and distinct binding profiles for each factor that were remodeled following TLR4 ligation. Development of a machine learning approach that jointly weighs hundreds of DNA recognition elements yields dozens of motifs predicted to drive factor-specific binding profiles. Machine learning-based predictions are confirmed by analysis of the effects of mutations in genetically diverse mice and by loss of function experiments. These findings provide evidence that non-redundant genomic locations of different AP-1 family members in macrophages largely result from collaborative interactions with diverse, locus-specific ensembles of transcription factors and suggest a general mechanism for encoding functional specificities of their common recognition motif.
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Affiliation(s)
- Gregory J Fonseca
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Emma M Westin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Sascha H Duttke
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Zeyang Shen
- Department of Bioengineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92037, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Verena M Link
- Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, 80539, Germany
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA.
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA.
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Link VM, Romanoski CE, Metzler D, Glass CK. MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. Nucleic Acids Res 2018; 46:7006-7021. [PMID: 29893919 PMCID: PMC6101580 DOI: 10.1093/nar/gky491] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/14/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
Cell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown. We have shown that natural genetic variation between individuals has great utility for discovering collaborative transcription factors. Here, we introduce MMARGE (Motif Mutation Analysis of Regulatory Genomic Elements), the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MMARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChIP-seq. Herein, we provide investigators with rationale for each step in the MMARGE pipeline and key differences for analysis of datasets with different experimental designs. We demonstrate the utility of MMARGE using mouse peritoneal macrophages, liver cells, and human lymphoblastoid cells. MMARGE provides a powerful tool to identify combinations of cell type-specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
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Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, USA
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian Universität München, Planegg-Martinsried, Germany
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, USA
| | - Dirk Metzler
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian Universität München, Planegg-Martinsried, Germany
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, USA
- Department of Medicine, University of California, San Diego, San Diego, USA
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29
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Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell 2018; 173:1796-1809.e17. [PMID: 29779944 PMCID: PMC6003872 DOI: 10.1016/j.cell.2018.04.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites, and transcription factor binding in resting and activated macrophages. We observed substantial differences associated with distinct molecular pathways. Evaluating genetic variation provided evidence for roles of ∼100 TFs in shaping lineage-determining factor binding. Unexpectedly, a substantial fraction of strain-specific factor binding could not be explained by local mutations. Integration of genomic features with chromatin interaction data provided evidence for hundreds of connected cis-regulatory domains associated with differences in transcription factor binding and gene expression. This system and the >250 datasets establish a substantial new resource for investigation of how genetic variation affects cellular phenotypes.
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Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Sascha H Duttke
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Inge R Holtman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Neuroscience, Section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emma Westin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dylan Skola
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Dirk Metzler
- Faculty of Biology, Division of Evolutionary Biology, Ludwig-Maximilian University of Munich, Munich, Germany
| | - Bing Ren
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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30
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Troutman TD, Seidman JS, Link VM, Hosseini M, Sakai M, Bruni C, Ouyang Z, Pasillas M, Glass CK. Hepatic Myeloid Cell Diversity During Fibrosis and Nonalcoholic Steatohepatitis. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.49.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Fatty liver diseases account for rapidly growing morbidity in the United States where it is estimated that 80 to 100 million individuals have non-alcoholic fatty liver disease (NAFLD), and 6 to 16 million have the more severe variant nonalcoholic steatohepatitis (NASH). The mechanisms underlying development of NASH and progression to cirrhosis are physiologically complex. Using scRNA-Seq, we profiled CD45+ cells from the livers of mice subjected to a dietary NASH model. This approach revealed that the NASH model diet induced transcriptional diversification of Kupffer cells, and resulted in expansion of myeloid cell types. Kupffer cells, defined as F4/80High CD11bIntermediate, play a key role in the development of liver disease through their role as sentinel cells. They respond to noxious stimuli by producing chemokines and cytokines, which promote both recruitment of inflammatory leukocytes and pro-fibrogenic activation of hepatic stellate cells. Through flow cytometry, we confirmed scRNA-Seq suggestions of hepatic macrophage diversification beyond the previously reported F4/80Low CD11bHigh Ly6CHigh and F4/80Low CD11bHigh Ly6CLow recruited macrophages. Further profiling of these hepatic macrophages by RNA-Seq suggested the differential involvement of these cell subsets in the disease process. These results were corroborated using an alternative mouse model of liver fibrosis. Ongoing experiments are targeted towards assessment of the developmental origin of the distinct Kupffer cell subsets, with preliminary data suggesting a monocytic and not embryonic origin. Further efforts are focused on comparisons of myeloid populations in humans and mouse towards informing the design of future experiments.
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31
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Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK. SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metab 2017; 25:412-427. [PMID: 28041958 PMCID: PMC5568699 DOI: 10.1016/j.cmet.2016.11.009] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/06/2016] [Accepted: 11/25/2016] [Indexed: 12/26/2022]
Abstract
Macrophages play pivotal roles in both the induction and resolution phases of inflammatory processes. Macrophages have been shown to synthesize anti-inflammatory fatty acids in an LXR-dependent manner, but whether the production of these species contributes to the resolution phase of inflammatory responses has not been established. Here, we identify a biphasic program of gene expression that drives production of anti-inflammatory fatty acids 12-24 hr following TLR4 activation and contributes to downregulation of mRNAs encoding pro-inflammatory mediators. Unexpectedly, rather than requiring LXRs, this late program of anti-inflammatory fatty acid biosynthesis is dependent on SREBP1 and results in the uncoupling of NFκB binding from gene activation. In contrast to previously identified roles of SREBP1 in promoting production of IL1β during the induction phase of inflammation, these studies provide evidence that SREBP1 also contributes to the resolution phase of TLR4-induced gene activation by reprogramming macrophage lipid metabolism.
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Affiliation(s)
- Yumiko Oishi
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department II, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Evan D Muse
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chantle Edillor
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew J Kolar
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, Graduate School of Comprehensive Human Sciences, International Institute for Integrative Sleep Medicine (WPI-IIIS), and Center for Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki Prefecture 305-8571, Japan
| | - Sumio Hayakawa
- Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minna U Kaikkonen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael T Lam
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ichiro Manabe
- Department of Aging Research, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, Graduate School of Comprehensive Human Sciences, International Institute for Integrative Sleep Medicine (WPI-IIIS), and Center for Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki Prefecture 305-8571, Japan
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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32
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Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK. Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. eLife 2016; 5. [PMID: 27462873 PMCID: PMC4963201 DOI: 10.7554/elife.13024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 06/30/2016] [Indexed: 12/24/2022] Open
Abstract
Although macrophages can be polarized to distinct phenotypes in vitro with individual ligands, in vivo they encounter multiple signals that control their varied functions in homeostasis, immunity, and disease. Here, we identify roles of Rev-erb nuclear receptors in regulating responses of mouse macrophages to complex tissue damage signals and wound repair. Rather than reinforcing a specific program of macrophage polarization, Rev-erbs repress subsets of genes that are activated by TLR ligands, IL4, TGFβ, and damage-associated molecular patterns (DAMPS). Unexpectedly, a complex damage signal promotes co-localization of NF-κB, Smad3, and Nrf2 at Rev-erb-sensitive enhancers and drives expression of genes characteristic of multiple polarization states in the same cells. Rev-erb-sensitive enhancers thereby integrate multiple damage-activated signaling pathways to promote a wound repair phenotype. DOI:http://dx.doi.org/10.7554/eLife.13024.001
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Affiliation(s)
- Dawn Z Eichenfield
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, United States
| | - Ty Dale Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department II, Faculty of Biology, Ludwig-Maximilian Universität München, Planegg-Martinsried, Germany
| | - Michael T Lam
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, United States.,Department of Medicine, University of California, San Diego, San Diego, United States
| | - Han Cho
- Salk Institute for Biological Sciences, La Jolla, United States
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Hanna P Lesch
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
| | - Jun Muto
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, San Diego, United States
| | - Ronald M Evans
- Salk Institute for Biological Sciences, La Jolla, United States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States.,Department of Medicine, University of California, San Diego, San Diego, United States
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33
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Link VM, Gosselin D, Glass CK. Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers. Cold Spring Harb Symp Quant Biol 2015; 80:213-21. [PMID: 26582787 DOI: 10.1101/sqb.2015.80.027367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Macrophages populate every tissue of the body and play vital roles in homeostasis, pathogen elimination, and tissue healing. These cells possess the ability to adapt to a multitude of abruptly changing and complex environments. Furthermore, different populations of resident tissue macrophages each show their own defining gene signatures. The enhancer repertoire of these cells underlies both the cellular identity of a given subset of resident macrophage population and their ability to dynamically alter, in an efficient manner, their gene expression programs in response to internal and external signals. Notably, transcription is pervasive at active enhancers and enhancer RNAs, or eRNAs, are tightly correlated to regulated transcription of protein-coding genes. Furthermore, selection and establishment of enhancers is a dynamic and plastic process in which activation of intracellular signaling pathways by factors present in a macrophage's environment play a determining role. Here, we review recent studies providing insights into the distinct mechanisms that contribute to the selection and function of enhancers in macrophages and the relevance of studying these mechanisms to gain a better understanding of complex human diseases.
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Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651 Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651 Department of Medicine, University of California, San Diego, La Jolla, California 92093-0651
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34
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Romanoski CE, Link VM, Heinz S, Glass CK. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol 2015; 36:507-18. [PMID: 26298065 DOI: 10.1016/j.it.2015.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/15/2015] [Accepted: 07/17/2015] [Indexed: 12/18/2022]
Abstract
The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.
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Affiliation(s)
- Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 85152, Germany
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
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